feat: init
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269
test/model/data_sources/test_bdv_data_source.py
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269
test/model/data_sources/test_bdv_data_source.py
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import os
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import pytest
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import numpy as np
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import h5py
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from navigate.tools.file_functions import delete_folder
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def recurse_dtype(group):
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for key, subgroup in group.items():
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subgroup_type = type(subgroup)
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if subgroup_type == h5py._hl.group.Group:
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recurse_dtype(subgroup)
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elif subgroup_type == h5py._hl.dataset.Dataset:
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if key == "resolutions":
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assert subgroup.dtype == "float64"
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elif key == "subdivisions":
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assert subgroup.dtype == "int32"
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elif key == "cells":
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assert subgroup.dtype == "uint16"
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else:
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print("Unknown how to handle:", key, subgroup_type)
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def bdv_ds(fn, multiposition, per_stack, z_stack, stop_early, size):
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from test.model.dummy import DummyModel
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from navigate.model.data_sources.bdv_data_source import BigDataViewerDataSource
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print(
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f"Conditions are multiposition: {multiposition} per_stack: {per_stack} "
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f"z_stack: {z_stack} stop_early: {stop_early}"
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)
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# Set up model with a random number of z-steps to modulate the shape
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model = DummyModel()
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z_steps = np.random.randint(1, 3)
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timepoints = np.random.randint(1, 3)
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x_size, y_size = size
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model.configuration["experiment"]["CameraParameters"]["x_pixels"] = x_size
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model.configuration["experiment"]["CameraParameters"]["y_pixels"] = y_size
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model.img_width = x_size
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model.img_height = y_size
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model.configuration["experiment"]["MicroscopeState"]["image_mode"] = (
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"z-stack" if z_stack else "single"
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)
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model.configuration["experiment"]["MicroscopeState"]["number_z_steps"] = z_steps
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model.configuration["experiment"]["MicroscopeState"][
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"is_multiposition"
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] = multiposition
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model.configuration["experiment"]["MicroscopeState"]["timepoints"] = timepoints
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model.configuration["experiment"]["BDVParameters"] = {
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"shear": {
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"shear_data": True,
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"shear_dimension": "YZ",
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"shear_angle": 45,
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},
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"rotate": {
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"rotate_data": False,
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"X": 0,
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"Y": 0,
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"Z": 0,
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},
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"down_sample": {
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"down_sample": False,
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"axial_down_sample": 1,
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"lateral_down_sample": 1,
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},
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}
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if per_stack:
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model.configuration["experiment"]["MicroscopeState"][
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"stack_cycling_mode"
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] = "per_stack"
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else:
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model.configuration["experiment"]["MicroscopeState"][
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"stack_cycling_mode"
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] = "per_slice"
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# Establish a BDV data source
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ds = BigDataViewerDataSource(fn)
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ds.set_metadata_from_configuration_experiment(model.configuration)
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# Populate one image per channel per timepoint
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n_images = ds.shape_c * ds.shape_z * ds.shape_t * ds.positions
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print(
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f"x: {ds.shape_x} y: {ds.shape_y} z: {ds.shape_z} c: {ds.shape_c} "
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f"t: {ds.shape_t} positions: {ds.positions} per_stack: {ds.metadata.per_stack}"
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)
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data = (np.random.rand(n_images, ds.shape_y, ds.shape_x) * 2**16).astype("uint16")
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dbytes = np.sum(
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ds.shapes.prod(1) * ds.shape_t * ds.shape_c * ds.positions * 2
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) # 2 bytes per pixel (16-bit)
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assert dbytes == ds.nbytes
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data_positions = (np.random.rand(n_images, 5) * 50e3).astype(float)
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for i in range(n_images):
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ds.write(
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data[i, ...].squeeze(),
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x=data_positions[i, 0],
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y=data_positions[i, 1],
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z=data_positions[i, 2],
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theta=data_positions[i, 3],
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f=data_positions[i, 4],
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)
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if stop_early and np.random.rand() > 0.5:
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break
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return ds
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def close_bdv_ds(ds, file_name=None):
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ds.close()
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if file_name is None:
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file_name = ds.file_name
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# Delete
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try:
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xml_fn = os.path.splitext(file_name)[0] + ".xml"
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if os.path.isdir(file_name):
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# n5 is a directory
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delete_folder(file_name)
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else:
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os.remove(file_name)
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os.remove(xml_fn)
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except PermissionError:
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# Windows seems to think these files are still open
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pass
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@pytest.mark.parametrize("multiposition", [True, False])
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@pytest.mark.parametrize("per_stack", [True, False])
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@pytest.mark.parametrize("z_stack", [True, False])
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@pytest.mark.parametrize("stop_early", [True, False])
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@pytest.mark.parametrize("size", [(1024, 2048), (2048, 1024), (2048, 2048)])
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@pytest.mark.parametrize("ext", ["h5", "n5"])
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def test_bdv_write(multiposition, per_stack, z_stack, stop_early, size, ext):
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fn = f"test.{ext}"
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ds = bdv_ds(fn, multiposition, per_stack, z_stack, stop_early, size)
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file_name = ds.file_name
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ds.close()
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# check datatypes
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# todo: extend to n5
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if ext == "h5":
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ds = h5py.File(f"test.{ext}", "r")
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for key in ds.keys():
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recurse_dtype(ds[key])
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close_bdv_ds(ds, file_name=file_name)
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assert True
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@pytest.mark.parametrize("multiposition", [True, False])
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@pytest.mark.parametrize("per_stack", [True, False])
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@pytest.mark.parametrize("z_stack", [True, False])
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@pytest.mark.parametrize("size", [(1024, 2048), (2048, 1024), (2048, 2048)])
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def test_bdv_getitem(multiposition, per_stack, z_stack, size):
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ds = bdv_ds("test.h5", multiposition, per_stack, z_stack, False, size)
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# Check indexing
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assert ds[0, ...].shape == (
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ds.positions,
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ds.shape_t,
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ds.shape_z,
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ds.shape_c,
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ds.shape_y,
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1,
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)
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assert ds[:, 0, ...].shape == (
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ds.positions,
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ds.shape_t,
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ds.shape_z,
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ds.shape_c,
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1,
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ds.shape_x,
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)
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assert ds[:, :, 0, ...].shape == (
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ds.positions,
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ds.shape_t,
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ds.shape_z,
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1,
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ds.shape_y,
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ds.shape_x,
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)
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assert ds[:, :, :, 0, ...].shape == (
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ds.positions,
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ds.shape_t,
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1,
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ds.shape_c,
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ds.shape_y,
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ds.shape_x,
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)
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assert ds[:, :, :, :, 0, ...].shape == (
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ds.positions,
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1,
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ds.shape_z,
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ds.shape_c,
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ds.shape_y,
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ds.shape_x,
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)
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assert ds[:, :, :, :, :, 0].shape == (
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1,
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ds.shape_t,
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ds.shape_z,
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ds.shape_c,
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ds.shape_y,
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ds.shape_x,
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)
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# Check slicing
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sx = 5
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assert ds[:sx, ...].shape == (
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ds.positions,
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ds.shape_t,
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ds.shape_z,
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ds.shape_c,
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ds.shape_y,
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min(ds.shape_x, sx),
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)
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assert ds[:, :sx, ...].shape == (
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ds.positions,
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ds.shape_t,
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ds.shape_z,
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ds.shape_c,
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min(ds.shape_y, sx),
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ds.shape_x,
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)
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assert ds[:, :, :sx, ...].shape == (
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ds.positions,
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ds.shape_t,
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ds.shape_z,
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min(ds.shape_c, sx),
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ds.shape_y,
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ds.shape_x,
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)
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assert ds[:, :, :, :sx, ...].shape == (
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ds.positions,
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ds.shape_t,
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min(ds.shape_z, sx),
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ds.shape_c,
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ds.shape_y,
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ds.shape_x,
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)
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assert ds[:, :, :, :, :sx, ...].shape == (
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ds.positions,
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min(ds.shape_t, sx),
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ds.shape_z,
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ds.shape_c,
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ds.shape_y,
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ds.shape_x,
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)
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assert ds[:, :, :, :, :, :sx].shape == (
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min(ds.positions, sx),
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ds.shape_t,
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ds.shape_z,
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ds.shape_c,
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ds.shape_y,
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ds.shape_x,
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)
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close_bdv_ds(ds)
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assert True
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